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Phylogenetic Analysis of the YDJ1 Family of Molecular Chaperones Cory L. Lewis1, Wesner Antoine1, Mark L. Johnston2, and Jan A. Miernyk1,2 1Department of Biochemistry, University of Missouri, Columbia, MO 65211, 2USDA, Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO 65211 Molecular chaperones mediate the correct folding and assembly of proteins. Chaperones do not direct folding intermediates into a particular molecular pathway. Rather, they reduce the diversion of folding intermediates into non-productive side reactions. They bind to and stabilize otherwise unstable protein conformations, and through a controlled cycle of release and rebinding facilitate expression of the folding information that is inherent in the primary amino acid sequence. Chaperones typically function as multi-component molecular machines. A prominent molecular chaperone machine comprises Hsp70, a J-domain protein, and one to five additional cohort proteins. A J-domain protein that is apparently ubiquitous in eukaryotes was first described in Saccharomyces cerevisiae, YDJ1. The YDJ1 protein includes several well-defined functional domains. Starting at the N-terminus the domains are: the J-domain itself, a Gly/Phe-rich flexible linker domain, a unique zinc-finger protein interaction domain, a dimerization domain, and finally a C-terminal -CaaX motif. Based upon the results of anonymous proteomic and transcript profiling experiments, YDJ1-orthologous proteins are the most abundant of the J-domain proteins. The RLM-RACE technique was used to isolate the missing 5'-end of YDJ1 orthologs from castor oil plants (Ricinus communis L.) and Leek (Allium ampeloprasum var. porrum (L.) J. Gay). The RACE products were cloned and sequenced. The castor and leek sequences, additional plant sequences, and sequences from fungi, protists, and animals were used in a meta-genomic phylogenetic reconstruction. In plants, two gene duplication events occurred prior to the separation into monocots and dicots. The first gave rise to DjA2 and DjA3. The subsequent duplication gave rise to DjA2A and DjA2B. A third, species-specific, gene duplication occurred after the separation of plants into monocots and dicots, and resulted in DjA2A-1 and -2, DjA2B-1 and -2, and